Just a quick query;

How does BOINC choose which work unit to run when it starts a new unit?

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Due to varying workunit sizes from several projects, each with varying deadlines, the default method is First In, First Out. If BOINC calculates that a workunit may miss a deadline for some reason, it will switch to Earliest Deadline First mode (in BOINC Manager, it will say "Running, High Priority") until BOINC estimates that all dangers of missing a deadline have passed, then it will switch back to FIFO.

There is no way to force one method over the other.

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To expand on what OzsFan said...

If you have more than one project, Boinc determines which project to run next based on how much work has been done for each projects and tries to maintain the resource share of the projects. It does this using a system of debt. It regularly check on these values and determines if it need to give time to another project.

For more detail on Boinc inner workings see Work Scheduler.

Within a single project the default is First In First Out.

Between projects on a CPU the default is Round Robin modified by resource share. Between projects on a GPU the default is First In First Out.

There is a high priority mode that kicks in if a task in a project is in danger of being late if run in the default order. In this case, the earliest deadline task from the set of projects with tasks that are in deadline trouble is run. If there is more than one CPU, each CPU will be scheduled into this mode independently. Similarly for GPUs.

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BOINC WIKI